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Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 2022年 20卷 3899-3910页

作者： Borges, Patricia T. Silva, Diogo Silva, Tomas F. D. Brissos, Vania Canellas, Marina Lucas, Maria Fatima Masgrau, Laura Melo, Eduardo P. Machuqueiro, Miguel Frazao, Carlos Martins, Ligia O. Univ NOVA Lisboa Inst Tecnol Quim & Biol Antonio Xavier Av Republ P-2780157 Oeiras Portugal Univ Lisbon Fac Ciencias BioISI Biosyst & Integrat Sci Inst P-1749016 Lisbon Portugal Zymvol Biomodeling Carrer Roc Boronat 117 Barcelona 08018 Spain Univ Autonoma Barcelona Dept Chem Bellaterra 08193 Spain Univ Algarve Ctr Ciencias Mar P-8005139 Faro Portugal

DyP-type peroxidases (DyPs) are microbial enzymes that catalyze the oxidation of a wide range of substrates, including synthetic dyes, lignin-derived compounds, and metals, such as Mn2+ and Fe2+, and have enormous biotechnological potential in biorefineries. However, many questions on the molecular basis of enzyme function and stability remain unanswered. In this work, high-resolution structures of PpDyP wild-type and two engineered variants (6E10 and 29E4) generated by directed evolution were obtained. The X-ray crystal structures revealed the typical ferredoxin-like folds, with three heme access pathways, two tunnels, and one cavity, limited by three long loops including catalytic residues. Variant 6E10 displays significantly increased loops' flexibility that favors function over stability: despite the considerably higher catalytic efficiency, this variant shows poorer protein stability compared to wild-type and 29E4 variants. Constant-pH MD simulations revealed a more positively charged microenvironment near the heme pocket of variant 6E10, particularly in the neutral to alkaline pH range. This microenvironment affects enzyme activity by modulating the pK(a) of essential residues in the heme vicinity and should account for variant 6E10 improved activity at pH 7-8 compared to the wild-type and 29E4 that show optimal enzymatic activity close to pH 4. Our findings shed light on the structure-function relationships of DyPs at the molecular level, including their pH-dependent conformational plasticity. These are essential for understanding and engineering the catalytic properties of DyPs for future biotechnological applications. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.

关键词： Biorefinery Biocatalysis Directed evolution Protein stability structure-function relationships

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Sequentially Regulating the Structural Transformation of Copper Metal-Organic Frameworks (Cu-MOFs) for Controlling Site-Selective Reaction

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ACS APPLIED MATERIALS & INTERFACES 2022年第32期14卷 36845-36854页

作者： Qin, Qi Wang, Di Shao, Zhichao Zhang, Yingying Zhang, Qiang Li, Xinyue Huang, Chao Mi, Liwei Zhongyuan Univ Technol Ctr Adv Mat Res Zhengzhou 450007 Peoples R China Zhongyuan Univ Technol Henan Key Lab Funct Salt Mat Zhengzhou 450007 Peoples R China

Regulating atomically precise sites in catalysts to achieve site-selective reactions is remarkable but challenging. In this work, a convenient and facile solid-gas/ liquid reaction strategy was used to construct controllable active sites in metal-organic frameworks (MOFs) to guide an orientation site-selective reaction. A flexible Cu-I-MOF-1 with dynamics originating from an anionic and tailorable framework could undergo a reversible structural transformation to engineer a topologically equivalent mixed-valent (CuCuII)-Cu-I-MOF-2 via a solid-gas/liquid oxidation/reduction process. More importantly, Cu-I-MOF-1 and (CuCuII)-Cu-I-MOF-2 could further execute the solid-gas/liquid reaction under ammonia vapor/solution to generate Cu-II-MOF-3. Furthermore, the transformation from Cu-I-MOF-1 to (CuCuII)-Cu-I-MOF-2 and Cu-II-MOF-3 served as controllable catalysts to facilitate site-selective reactions to realize direct C-N bond arylations. The results demonstrated that Cu-I-MOF-1 and Cu-II-MOF-3 possessed well-defined platforms with uniformly and accurately active sites to attain a "turn-on/off " process via different reaction routes, providing the desired site-selective ring-opening products.

关键词： metal-organic frameworks structural transformation solid-gas liquid reaction structure-function relationships site-selective reaction

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Enhancement of Output Performance of Triboelectric Nanogenerator by Switchable Stimuli in Metal-Organic Frameworks for Photocatalysis

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ACS APPLIED MATERIALS & INTERFACES 2022年第14期14卷 16424-16434页

作者： Huang, Chao Lu, Guizhen Qin, Na Shao, Zhichao Zhang, Dianbo Soutis, Constantinos Zhang, Ying-Ying Mi, Liwei Hou, Hongwei Zhongyuan Univ Technol Ctr Adv Mat Res Zhengzhou 450007 Peoples R China Zhongyuan Univ Technol Henan Key Lab Funct Salt Mat Zhengzhou 450007 Peoples R China Univ Manchester North West Composites Ctr Sch Mat Manchester M13 9PL Lancs England Zhengzhou Univ Coll Chem & Green Catalysis Ctr Zhengzhou 450001 Peoples R China

Precise control of the structure of crystalline materials is an efficient strategy to manipulate the fundamental performance of solids. In metal-organic framework (MOF) materials, this control can be realized by reversible cation-exchange through chemically driven changes in the crystalline state. Herein, we reported that the reversible structural transformations between an anionic Zn-MOF (1) and a topologically equivalent bimetallic Zn/Co-MOF (2) were accomplished. Both MOFs powders and their hybrid composites were used as positive electrode materials to assemble triboelectric nanogenerators (TENGs). The results demonstrated that the output performance of the Zn/Co-MOF-TENG was effectively improved because the introduction of Co ions makes electron transfer easier. Moreover, the output performance of the TENGs based on MOF@PVDF (PVDF = polyvinylidene fluoride) composite films showed that the Zn/Co-MOF@PVDF-TENG possessed much higher output than these corresponding film-based and MOF-based TENGs. As a practical application, the superior output of Zn/CoMOF@PVDF-TENG was used to light an ultraviolet lamp plate for the [2 + 2] photochemical cycloaddition of organometallic macrocycles.

关键词： metal-organic frameworks reversible SC-SC transformations [2+2] photochemical cycloaddition structure-function relationships triboelectric nanogenerators

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Prediction of visual field defects from macular optical coherence tomography in glaucoma using cluster analysis

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OPHTHALMIC AND PHYSIOLOGICAL OPTICS 2022年第5期42卷 948-964页

作者： Tong, Janelle Alonso-Caneiro, David Kalloniatis, Michael Zangerl, Barbara Univ New South Wales UNSW Ctr Eye Hlth Sydney NSW Australia Univ New South Wales UNSW Sch Optometry & Vis Sci Sydney NSW Australia Queensland Univ Technol Ctr Vis & Eye Res Sch Optometry & Vis Sci Contact Lens & Visual Opt Lab Kelvin Grove Qld Australia Royal Prince Alfred Hosp Coronary Care Unit Sydney NSW Australia

Purpose To assess the accuracy of cluster analysis-based models in predicting visual field (VF) defects from macular ganglion cell-inner plexiform layer (GCIPL) measurements in glaucomatous and healthy cohorts. Methods GCIPL measurements were extracted from posterior pole optical coherence tomography (OCT), from locations corresponding to central VF test grids. Models incorporating cluster analysis methods and corrections for age and fovea to optic disc tilt were developed from 493 healthy participants, and 5th and 1st percentile limits of GCIPL thickness were derived. These limits were compared with pointwise 5th and 1st percentile limits by calculating sensitivities and specificities in an additional 40 normal and 37 glaucomatous participants, as well as applying receiver operating characteristic (ROC) curve analyses to assess the accuracy of predicting VF results from co-localised GCIPL measurements. Results Clustered models demonstrated globally low sensitivity, but high specificity in the glaucoma cohort (0.28-0.53 and 0.77-0.91, respectively), and high specificity in the healthy cohort (0.91-0.98). Clustered models showed similar sensitivities and superior specificities compared with pointwise methods (0.41-0.65 and 0.71-0.98, respectively). There were significant differences in accuracy between clusters, with relatively poor accuracy at peripheral macular locations (p < 0.0001 for all comparisons). Conclusions Cluster analysis-based models incorporating age correction and holistic consideration of fovea to optic disc tilt demonstrated superior performance in predicting VF results to pointwise methods in both glaucomatous and healthy eyes. However, relatively low sensitivity and poorer performance at the peripheral macula indicate that OCT in isolation may be insufficient to predict visual function across the macula accurately. With modifications to criteria for abnormality, the concepts suggested by the described normative models may guide prioritisation of V

关键词： glaucoma optical coherence tomography structure-function relationships visual fields

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structure-function relationships in conjugated materials containing tunable thieno[3,4-b]pyrazine units

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POLYMER BULLETIN 2012年第3期69卷 291-301页

作者： Mulholland, Michael E. Schwiderski, Ryan L. Rasmussen, Seth C. N Dakota State Univ NDSU Dept 2735 Dept Chem & Biochem Fargo ND 58108 USA

A series of 2,3-difunctionalized 5,7-bis(2-thienyl)thieno[3,4-b]pyrazines containing electron-donating and electron-withdrawing side chains are reported to evaluate the potential tuning effect of the side chains on the electronic properties of these common terthienyl building blocks. In order to further study the resulting effects of such side chains in polymeric materials, the dihexyloxy-functionalized terthienyl was copolymerized with fluorene and its electronic properties compared with a number of analogous materials.

关键词： Conjugated polymers Thieno[3,4-b]pyrazine structure-function relationships Electronic tuning

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Tyrosine 288 in the extracellular domain of the human P2X7 receptor is critical for receptor function revealed by structural modeling and site-directed mutagenesis

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PROTEINS-structure function AND BIOINFORMATICS 2022年第3期90卷 619-624页

作者： Caseley, Emily A. Muench, Stephen P. Jiang, Lin-Hua St James Univ Hosp Leeds Inst Rheumat & Musculoskeletal Med Leeds W Yorkshire England Univ Leeds Fac Biol Sci Sch Biomed Sci Leeds LS2 9JT W Yorkshire England

The P2X7 receptor (P2X7R) is a calcium-permeable cation channel activated by high concentrations of extracellular ATP. It plays a role in vital physiological processes, particularly in innate immunity, and is dysregulated in pathological conditions such as inflammatory diseases, neurodegenerative diseases, mood disorders, and cancers. Structural modeling of the human P2X7R (hP2X7R) based on the recently available structures of the rat P2X7 receptor (rP2XR) in conjunction with molecular docking predicts the orientation of tyrosine at position 288 (Y288) in the extracellular domain to face ATP. In this short communication, we combined site-directed mutagenesis and whole-cell patch-clamp recording to investigate the role of this residue in the hP2X7R function. Mutation of this extracellular residue to amino acids with different properties massively impaired current responses to both ATP and BzATP, suggesting that Y288 is important for normal receptor function. Such a finding facilitates development of an in-depth understanding of the molecular basis of hP2X7R structure-function relationships.

关键词： molecular docking patch-clamp recording site-directed mutagenesis structural modeling structure-function relationships

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Materiomically Designed Polymeric Vehicles for Nucleic Acids: Quo Vadis?

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ACS APPLIED BIO MATERIALS 2022年第6期5卷 2507-2535页

作者： Kumar, Ramya Colorado Sch Mines Dept Chem & Biol Engn Golden CO 80401 USA

Despite rapid advances in molecular biology, particularly in site-specific genome editing technologies, such as CRISPR/Cas9 and base editing, financial and logistical challenges hinder a broad population from accessing and benefiting from gene therapy. To improve the affordability and scalability of gene therapy, we need to deploy chemically defined, economical, and scalable materials, such as synthetic polymers. For polymers to deliver nucleic acids efficaciously to targeted cells, they must optimally combine design attributes, such as architecture, length, composition, spatial distribution of monomers, basicity, hydrophilic-hydrophobic phase balance, or protonation degree. Designing polymeric vectors for specific nucleic acid payloads is a multivariate optimization problem wherein even minuscule deviations from the optimum are poorly tolerated. To explore the multivariate polymer design space rapidly, efficiently, and fruitfully, we must integrate parallelized polymer synthesis, high-throughput biological screening, and statistical modeling. Although materiomics approaches promise to streamline polymeric vector development, several methodological ambiguities must be resolved. For instance, establishing a flexible polymer ontology that accommodates recent synthetic advances, enforcing uniform polymer characterization and data reporting standards, and implementing multiplexed in vitro and in vivo screening studies require considerable planning, coordination, and effort. This contribution will acquaint readers with the challenges associated with materiomics approaches to polymeric gene delivery and offers guidelines for overcoming these challenges. Here, we summarize recent developments in combinatorial polymer synthesis, high-throughput screening of polymeric vectors, omits-based approaches to polymer design, barcoding schemes for pooled in vitro and in vivo screening, and identify materiomics-inspired research directions that will realize the long-unfulfilled clini

关键词： nucleic acid delivery genome editing nonviral gene delivery polymers machine learning controlled radical polymerization high-throughput experimentation structure-function relationships

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Exopolysaccharide production by salt-tolerant bacteria: Recent advances, current challenges, and future prospects

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INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 2024年第Part2期264卷 130731页

作者： Gan, Longzhan Huang, Xin He, Zhicheng He, Tengxia Guizhou Univ Coll Life Sci Key Lab Plant Resource Conservat & Germplasm Innov Minist Educ Guiyang 550025 Guizhou Peoples R China

Natural biopolymers derived from exopolysaccharides (EPSs) are considered eco-friendly and sustainable alternatives to available traditional synthetic counterparts. Salt-tolerant bacteria inhabiting harsh ecological niches have evolved a number of unique adaptation strategies allowing them to maintain cellular integrity and assuring their long-term survival;among these, producing EPSs can be adopted as an effective strategy to thrive under high-salt conditions. A great diversity of EPSs from salt-tolerant bacteria have attracted widespread attention recently. Because of factors such as their unique structural, physicochemical, and functional characteristics, EPSs are commercially valuable for the global market and their application potential in various sectors is promising. However, large-scale production and industrial development of these biopolymers are hindered by their low yields and high costs. Consequently, the research progress and future prospects of salt-tolerant bacterial EPSs must be systematically reviewed to further promote their application and commercialization. In this review, the structure and properties of EPSs produced by a variety of salt-tolerant bacterial strains isolated from different sources are summarized. Further, feasible strategies for solving production bottlenecks are discussed, which provides a scientific basis and direct reference for more scientific and rational EPS development.

关键词： Biopolymer Exopolysaccharide Extremophile Salt-tolerant bacteria Biosynthesis structure-function relationships Production strategy

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Chitosan-Polyaniline (Bio)Polymer Hybrids by Two Pathways: A Tale of Two Biocomposites

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POLYMERS 2024年第18期16卷 2663页

作者： Anisimov, Yuriy A. Yang, Heng Kwon, Johnny Cree, Duncan E. Wilson, Lee D. McMaster Univ Dept Chem Engn Hamilton ON L8S 4M6 Canada Univ Saskatchewan Dept Chem 110 Sci Pl Saskatoon SK S7N 5C9 Canada McMaster Univ Dept Mech Engn Hamilton ON L8S 4L8 Canada

Previous research highlights the potential of polyaniline-based biocomposites as unique adsorbents for humidity sensors. This study examines several preparative routes for creating polyaniline (PANI) and chitosan (CHT) composites: Type 1-in situ polymerization of aniline with CHT;Type 2-molecular association in acidic aqueous media;and a control, Type 3-physical mixing of PANI and CHT powders (without solvent). The study aims to differentiate the bonding nature (covalent vs. noncovalent) within these composites, which posits that noncovalent composites should exhibit similar physicochemical properties regardless of the preparative route. The results indicate that Type 1 composites display features consistent with covalent and hydrogen bonding, which result in reduced water swelling versus Type 2 and 3 composites. These findings align with spectral and thermogravimetric data, suggesting more compact structure for Type 1 materials. Dye adsorption studies corroborate the unique properties for Type 1 composites, and H-1 NMR results confirm the role of covalent bonding for the in situ polymerized samples. The structural stability adopts the following trend: Type 1 (covalent and noncovalent) > Type 2 (possible trace covalent and mainly noncovalent) > Type 3 (noncovalent). Types 2 and 3 are anticipated to differ based on solvent-driven complex formation. This study provides greater understanding of structure-function relationships in PANI-biopolymer composites and highlights the role of CHT as a template that involves variable (non)covalent contributions with PANI, according to the mode of preparation. The formation of composites with tailored bonding modalities will contribute to the design of improved adsorbent materials for environmental remediation to versatile humidity sensor systems.

关键词： polyaniline-chitosan composites covalent bonding noncovalent interactions structure-function relationships

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Recent advances in dietary polysaccharides from Allium species: Preparation, characterization, and bioactivity

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INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 2024年第Part1期277卷 134130页

作者： Yu, Ya-Hui Liu, Fengyuan Li, Long-Qing Jin, Ming-Yu Yu, Xiangying Liu, Xiaozhen Li, Yuting Li, Lin Yan, Jing-Kun Dongguan Univ Technol Sch Life & Hlth Technol Dongguan Key Lab Typ Food Precis Design China Natl Light Ind Key Lab Hlth Food Dev & Nutr Dongguan 523808 Peoples R China

Allium plants, including garlic, onions, shallots, and leeks, belong to the Alliaceae family and are utilized as vegetable, medicinal, and ornamental plants. These plants are consumed both raw and cooked and are noted in traditional medicine for their antibacterial, antitumor, and diuretic properties. Allium plants are a rich source of polyphenols, organosulfur compounds, flavonoids, alkaloids, and polysaccharides, which contribute to their health benefits. As consumer interest in the association between diet and health grows, there is an increasing market demand for foods that promote health, particularly those rich in dietary fiber or non-starch polysaccharides. Allium polysaccharides (APS) have molecular weights of 1 x 103-1 x 106 Da containing small amounts of pectin, glucofructan, or glycoproteins and large amounts of fructans. APS, despite its complex structure, is one of the principal active components of Allium plants but is often overlooked, which restricts its practical application. This paper provides a comprehensive overview of the extraction and purification, structural and functional characteristics, bioactivities, structure-function relationships, and chemical modifications of APS, as well as the effects of APS processing and storage. Additionally, this paper outlines future research directions for APS, which will inform its development and application in the food, pharmaceutical, and cosmetic industries.

关键词： Allium polysaccharides Structural characteristics structure-function relationships

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